Hi, I did some more testing to see what could be the problem. The main weird thing I see is that in the coords_for_fdt_matrix3 file, there are some strange values: coords_for_fdt_matrix3 : 309 -57 38 0 8341 308 -57 38 0 8342 307 -56 38 0 8343 306 -55 37 0 8344 306 -55 36 0 8345 305 -55 36 0 8346 304 -55 35 0 8347 304 -54 34 0 8348 tract_space_coords_for_fdt_matrix3: 263 -44 30 0 0 276 -40 72 0 1 311 -5 42 0 2 266 27 59 0 3 286 -90 23 0 4 313 -52 47 0 5 292 52 5 0 6
If the first 3 values are x-y-z then this is somewhere outside the brain probably. However, when I use the L.STS.fsl_MNI_new.asc and brainmap_filelist.txt inputs as seeds (-x ) without any matrix options, the outputs (as in fdt_paths.nii.gz) look like expected. So this would indicate that there is no problem in transforming the seeds to dti space and reading them I would think? Any suggestions? -Maarten On Mon, Jul 20, 2015 at 6:29 PM, Maarten Vaessen <[email protected]> wrote: > Ah, of course! > That is: > > wb_command -probtrackx-dot-convert fdt_matrix3.dot > test_dot_to_cifti.dconn.nii -col-surface L.STS.func.gii -row-cifti > 91282_Greyordinates.dscalar.nii COLUMN -transpose > > On Mon, Jul 20, 2015 at 5:54 PM, Glasser, Matthew <[email protected] > > wrote: > >> No I meant the dot convert. >> >> Matt. >> >> From: Maarten Vaessen <[email protected]> >> Date: Monday, July 20, 2015 at 3:29 AM >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] tractography >> >> The conversion was done like this: >> >> wb_command -gifti-label-to-roi >> ../../MNINonLinear/fsaverage_LR32k/102816.L.aparc.a2009s.32k_fs_LR.label.gii >> L.STS.func.gii -name S_temporal_sup >> surf2surf -i >> ../../MNINonLinear/fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -o >> L.STS.fsl_MNI_new.asc --outputtype=ASCII --values=L.STS.func.gii >> >> Is this what you were referring to? >> >> -Maarten >> >> On Sun, Jul 19, 2015 at 10:20 PM, Glasser, Matthew < >> [email protected]> wrote: >> >>> The --onewaycondition flag doesn’t seem sensible with matrix3. Also I >>> don’t know what your command was for doing the conversion. Here is the >>> probtrackx2 call that didn’t make it onto the list: >>> >>> probtrackx2 -x L.STS.fsl_MNI_new.asc --onewaycondition --omatrix3 >>> --target3=L.STS.fsl_MNI_new.asc >>> --lrtarget3=brainmap_HCP/brainmap_filelist.txt -P 100 --forcedir >>> --dir=./test_surf_track_STS_brainmap_seedspace -s >>> ../Diffusion.bedpostX/merged -m nodif_brain_mask.nii.gz >>> --seedref=../../MNINonLinear/T1w_restore.nii.gz -V 2 --opd --pd >>> --distthresh3=2 --xfm=../../MNINonLinear/xfms/standard2acpc_dc.nii.gz >>> --invxfm=../../MNINonLinear/xfms/acpc_dc2standard.nii.gz >>> >>> >>> Peace, >>> >>> >>> Matt. >>> >>> From: Maarten Vaessen <[email protected]> >>> Date: Sunday, July 19, 2015 at 12:03 PM >>> To: Matt Glasser <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> Subject: Re: FW: [HCP-Users] tractography >>> >>> In this case: seed region to whole brain connectivity. The STS seed >>> is mainly for testing purposes (not as many seed points as the whole WM), >>> the final analysis will use all WM voxels as seeds though. In fact,when I >>> run the analysis with WM as the seed the results look equally strange: only >>> connectivity to what appears to be the right inferior posterior cortex. >>> Could this be an issue with the seed-space to dti-space parameters? >>> >>> -M >>> >>> On Sun, Jul 19, 2015 at 5:31 PM, Glasser, Matthew < >>> [email protected]> wrote: >>> >>>> What is it that you are trying to achieve? Usually one uses a seed >>>> of all white matter voxels with matrix3. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Maarten Vaessen <[email protected]> >>>> Date: Sunday, July 19, 2015 at 3:41 AM >>>> To: Matt Glasser <[email protected]> >>>> Subject: Re: [HCP-Users] tractography >>>> >>>> Hi Matthew, >>>> >>>> I tried to use the file you suggested, and I can convert the .dot >>>> without problem. However, the results don't make any sense, so I think >>>> there might be something wrong in my processing pipeline. Would you mind >>>> having a quick look at it and see if I do something wrong? >>>> Attached is the pipeline and a screenshot from the matrix as loaded in >>>> MATLAB. >>>> As you can see from the screenshot, there is only very limited number >>>> of none zeros. And weirdest of all, they appear at column indices which are >>>> probably somewhere in the right hemisphere (seed is in the left). >>>> >>>> Thanks, >>>> >>>> -Maarten >>>> >>>> On Wed, Jul 15, 2015 at 6:20 PM, Glasser, Matthew < >>>> [email protected]> wrote: >>>> >>>>> You should be able to use this file: >>>>> >>>>> >>>>> https://github.com/Washington-University/Pipelines/blob/master/global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: <[email protected]> on behalf of Maarten >>>>> Vaessen <[email protected]> >>>>> Date: Wednesday, July 15, 2015 at 4:44 AM >>>>> To: "[email protected]" <[email protected]> >>>>> Subject: Re: [HCP-Users] tractography >>>>> >>>>> Hello, >>>>> >>>>> >>>>> I followed the guide lines below to create a dense connectome with >>>>> probtrackx. I was just wondering how to proceed with converting the .dot >>>>> file from probtrackx to cifti using wb_command -probtrackx-dot-convert >>>>> (for visualisation in wb_view). Specifically, what cifti file can I use >>>>> as input for the -row-cifti option? So, what files released with the HCP >>>>> data contain the correct brainmap? >>>>> >>>>> >>>>> Thx >>>>> >>>>> >>>>> -Maarten >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________________________ >>>>> >>>>> Hi >>>>> >>>>> You need to create such a file that contains the 90k grayordinates. To >>>>> ensure >>>>> consistency we do that in MNI 2mm space: >>>>> >>>>> - First create surface files in an FSL friendly format. Use the 32k >>>>> surfaces, >>>>> as the vertices are ~2mm apart. >>>>> Left Surface: >>>>> surf2surf -i >>>>> $Subject/MNINonLinear/fsaverage_LR32k/${Subject}.L.white.32k_fs_LR.surf.gii >>>>> -o >>>>> white.L.asc --outputtype=ASCII >>>>> --values=$Subject/MNINonLinear/fsaverage_LR32k//${Subject}.L.atlasroi.32k_fs_LR.shape.gii >>>>> >>>>> Right Surface: >>>>> surf2surf -i >>>>> $Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii >>>>> -o >>>>> white.R.asc --outputtype=ASCII >>>>> --values=$Subject/MNINonLinear/fsaverage_LR32k//${Subject}.R.atlasroi.32k_fs_LR.shape.gii >>>>> >>>>> - Then extract the volume subcortical files from e.g. >>>>> $Subject/MNINonLinear/ROIs/Atlas_Rois.2.nii.gz, let’s say as >>>>> CIFTI_Structure_{Name}.nii.gz, using e.g. fslmaths or your favourite tool >>>>> for >>>>> ROI extraction. You should get 19 of these NIFTI files. (You can >>>>> obviously use >>>>> your favourite subcortical parcellation here, but if you want consistency >>>>> with >>>>> the CIFTI standard grayordinates, you need to resample the final results, >>>>> the >>>>> file above ensures consistency). >>>>> >>>>> - Put all the filenames in a text file in the following sequence, to >>>>> ensure >>>>> consistency with the rest of the CIFTIs: >>>>> >>>>> white.L.asc >>>>> white.R.asc >>>>> CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_ACCUMBENS_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_AMYGDALA_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_AMYGDALA_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_BRAIN_STEM.nii.gz >>>>> CIFTI_STRUCTURE_CAUDATE_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_CAUDATE_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_CEREBELLUM_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_CEREBELLUM_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_HIPPOCAMPUS_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_HIPPOCAMPUS_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_PALLIDUM_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_PALLIDUM_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_PUTAMEN_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_PUTAMEN_RIGHT.nii.gz >>>>> CIFTI_STRUCTURE_THALAMUS_LEFT.nii.gz >>>>> CIFTI_STRUCTURE_THALAMUS_RIGHT.nii.gz >>>>> >>>>> >>>>> - You can then use such a file in FSL probtrackx2 as a seed (for Matrix1) >>>>> or as >>>>> a target3 (for Matrix3). Notice that running a single probtrackx2 command >>>>> with >>>>> all these seed locations and with many samples per location will require >>>>> huge >>>>> processing power and memory. In practice, we run multiple probtrackx2 in >>>>> parallel, by splitting and parallelising the computation by using the >>>>> --rseed >>>>> option in probtrackx2 and using a small number of samples --nsamples per >>>>> instance. I.e. instead of running one command, which will attempt to >>>>> propagate >>>>> 5000 curves per seed, we can run e.g. 100 instances of the above commands, >>>>> using --nsamples=50 and --rseed=i, i=1..100. Results can then be combined >>>>> using >>>>> fdt_matrix_merge (which however also needs quite a lot of memory to >>>>> produce the >>>>> final dense connectomes, but at least it is one final process). >>>>> >>>>> - Another approach for parallelisation would be to split the seed >>>>> locations and >>>>> merge the final matrices. There is no solution that fits all systems, you >>>>> should try and find the best approach depending on your computing >>>>> resources. >>>>> >>>>> Hope this helps >>>>> Stam >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 19 May 2015, at 01:01, David R. Haynor >>>>> <[email protected]<mailto:[email protected] <[email protected]>>> >>>>> wrote: >>>>> >>>>> hi HCP, >>>>> >>>>> we are trying to do tractography using FSL and HCP data. i have some >>>>> questions >>>>> -- i suspect they have been answered already, but couldn't find those >>>>> answers: >>>>> >>>>> 1. is there a file containing the grayordinate coordinates in the >>>>> diffusion >>>>> space for a particular subject, both subcortical voxels and cortical >>>>> vertices? >>>>> >>>>> 2. if i want to use some cortical and subcortical voxels from the list of >>>>> grayordinates as targets, do i have to run probtrackx2 twice (i.e. once >>>>> for the >>>>> cortical surface vertices and once for the subcortical voxels), or can i >>>>> run it >>>>> just once? >>>>> >>>>> 3. where is the label file for the grayordinate vertices/voxels for a >>>>> given >>>>> subject? >>>>> >>>>> thanks in advance. >>>>> >>>>> -dh >>>>> _______________________________________________ >>>>> HCP-Users mailing >>>>> [email protected]<mailto:[email protected] >>>>> <[email protected]>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing >>>>> [email protected]http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> The materials in this message are private and may contain Protected >>>>> Healthcare Information or other information of a sensitive nature. 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